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Lecture 2- Nucleic Acid Structure Forces stabilizing DNA Forces stabilizing DNA Van der Waals Interactions Hydrophobic Effect -Electrostatic interaction between two mutually induced dipoles -Describes tendency of hydrophobic molecules to transfer from aqueous phase to organic phase E= -B + r6 B (A6.kcal/mol) Atom Lennard-Jones Potential H 46 O 220 OH 470 CH2 1160 S 3760 SH 4560 A r12 B is a function of polarizability Benzene crystal VdW Energy -9.9 kcal/mol H O H O H H H O H (1) Iceberg-like structure of water around organic solute: All four hydrogen bonds formed/ high order-entropic rerdty (In liquid water: roughly 1/2 hydrogen bonds formed) (2) poor polarizability of oxygen organic molecule tends to decreased VdW interaction between water and aggregate in water to organic solute minimize hydrophobic effect also drives hydrophobic effect E (kcal/mol) 0 VdW radii (Å) Atom Van der Waals radius 1.5 RO H O CH4-CH4 R2 R1 3.7 Å r 1.5 S R 1.5 O O -0.2 R1 N H R2 1.55 1.65 CH (tet) 1.85 CH (tri) 1.7 R R1 S R2 1.8 =P -Energetic contribution due to substituent -R groups have a constant additive effect on hydrophobicity of parent compound in absence of strong resonance/inductive effects Group NH3+ Solubility in octanol Solubility in water G = transfer from n-octanol to water G = RT log P/P0 O R VdW distance = VdWradii -Measurement of hydrophobicity is partitioning of molecule between n-octanol and H2O Solubility in octanol = P0 S H Solubility in water G (kcal/mol) -CH4 0.68 -Et 1.36 -propyl 2.05 -isopropyl 1.77 Group -benzyl -OH O G (kcal/mol) 3.6 -1.58 -1.65 N H 1 A2 of hydrophobic surface ca. 24 cal/mol stabilization when removed from H2O -Hydrophobic Effect can be relatively non-specific when molecules bind to protein or DNA Lecture 2- Nucleic Acid Structure Environmental Effect on pKas Forces stabilizing DNA pKa % dioxane in H2O Electrostatic Interaction -Proportional to 1/r; Long distance interaction compared to VdW e1 e2 E= H Dr e 0 20 45 70 acetic acid (CH3CO2H) 4.76 5.29 6.31 8.34 glycine (NH3+) 9.8 9.3 8.5 7.42 3.3 Å D is dielectric constant -Leveling Effect -Point charge induces dipoles in solvent which together with counterions induce field to neutralize charge D water ~ 80 -1.3 kcal/mol (very small) D pentane ~ 2 --50 kcal/mol Metal ion coordination stabilizes DNA Mg2+ -So electrostatic interactions are far more important in organic solvent than water. HN pKa2 ~ 3 Mn2+ Zn2+ Cd2+ Cu2+ (Hard) (Soft) Bind -OH/-PO4- Bind Bases Duplex DNA G = -RT logK G ca. 8.4 kcal/mol pKa ~ 6 N G = -RT logK = -1.4 logK kcal/mol (room temp) -1.4 kcal/mol for Product/Substrate = 10 O O 5' B1 G= = -1.4 log(K2/K1) at room temp G G=1 G=2 G product Progress of Reaction B3 O O O P OO O O P O O O G= 3' 5'-GCAT...... 3'-CGTA...... 3' O transition state substrate Ni2+ pKa1 ~ 8.8 NH HN Co2+ B2 B4 Always specify directionality of DNA sequence 5' O O O = -1.4 kcal/mol for a 10 fold difference in rate A A-T pair: Minor Groove D O NH N H2N A N N N N O A A Major Groove Lecture 2- Nucleic Acid Structure Duplex DNA (continue) Helix formation is cooperative Major Groove NH2 A O A N G-C pair: N N HN N N O A H2N A U U U U U K= S A U A U A U A U A U K=S A U A U A U A U A U ...... D Minor Groove B form DNA (dominant form) -Right handed under physiological conditions -10 bp/turn -3.3 Å/bp -helix axis through center of bp -anti -C2' endo -wide major groove - binds peptides -narrow minor groove - binds planar molecules A form DNA -Right handed (more contact) -11 bp/turn -2.3 Å/bp (short/broader) -24 Å/turn -major groove (deep narrow)/minor groove (broad shallow) -anti -C3' endo Z form DNA -Left handed -12 bp/turn -3.8 Å/bp -anti C/Syn G -no major groove/minor groove (deep narrow) A form RNA -C3' endo -RNA can adapt more distinct structures than DNA Single-stranded RNA A form DNA-RNA duplexes A form DNA duplexes A A A A A A form = 10-3 M-1 at 0 oC S = 10 at 0 oC -Helix coil transition is highly cooporative and nucleates by 3 bps Melting Temperature Tm -Tm characterizes the stability of double helix ssDNA A260 D -Melting duplex to singlestranded is accompanied by an increase in absorbance -Tm depends on length, ionic strength and GC/AT ratio Tm calculator: + 2 oC A-T pair + 4 oC A-T pair duplex Tm RNA secondary structure single strand A-form double helix single nt bulge hairpin loop mismatch pair symmetric internal loop -Secondary RNA structure can be predicted three nt bulge asymmetric internal loop -tertiary RNA structure is hard to be predicted Lecture 2- Nucleic Acid Structure DNA-binding small molecules Electrostatic Interaction -target phosphated sugar backbone H2 N H3N N H2 Higher order of DNA structure -Supercoiling Linear DNA NH3 spermine Intercalation H2N Unwound circle -targets G-C rich regions NH2 -Kd 10-6 M-1 -binds DNA from the narrow groove N negative supercoil DNA (Right-handed) Br -2 supercoil (neg) ~ 2 linear base Enzymes to control winding and unwinding of DNA -Topoisomerase (wind and unwind DNA) target for cancer drug G G C C G H2N Packing of chromosomal DNA C NH2 3.3 Å BrH G helix becomes slightly unwinded -DNA is packaged into chromatin in mammalian cells -duplex DNA tightly binds to 5 histones Cancer drug - Doxorubicin O DNA H2A X 2 packing ratio H2B X 2 is 104 in H3 X 2 human H4 X 2 genome 10-20 kDa N bind 3.3 Å C OH O OH OH 55 Å H1 680 Å into ~110 Å leads to packing ratio of 7 O O OH OSugar Doxorubicin 110 Å -Modulate duplex DNA and histone Interaction -acetylation of lysine (positive charge of histone proteins~ neutralized) -other post-translational modifications (PTMs) exist for modulating histone/DNA interaction -DNA is a popular target for cancer drugs as rapidly proliferating cells need to replicate DNA faster -binds DNA from minor groove -cancer drug -when Topo unwinds DNA, dox stablizes single strand DNA intermediate